The most important section of the Pipeworks manifest to understand is WebCommand. Without putting anything in WebCommand, your PowerShell scripts will not be able to be run as software services.
WebCommand is a hashtable containing the names of the commands you will turn into web services, and arguments to the command Invoke-WebCommand. Invoke-WebCommand is the command that runs an individual PowerShell cmdlet as a web service, in all of it's varieties.
For instance, the Pipeworks Quickstart contains a simple example function, Show-HelloMessage, and this simple command to create a Pipeworks manifest and run it.